The femtosecond transient absorption (TA) characterization of a new benzothiadiazole (BT)-based donor-acceptor conjugated copolymer, poly[(2,6-dithieno[3,2-b:2',3'-d]-thiophene)- alt-(4,7-di(4-octyldodecylthiopen-2-yl)-2,1,3-benzo[c][1,2,5] thiadiazole (PBT), as well as its fluorinated derivatives, PFBT and PDFBT, is carried out. Additionally, bulk heterojunction (BHJ) films consisting of the copolymers and [6,6]-phenyl-C-71-butylic acid methyl ester (PC70BM) are examined using TA spectroscopy. Both the singlet excited state dynamics in the copolymers and the charge transfer state dynamics in the BHJs are investigated in terms of fluorination dependency; the fluorinated copolymers exhibit less singlet exciton recombination rate than the fluorine-free copolymer, and the BHJs including the fluorinated copolymers display slower monomolecular recombination than the fluorine-free analogue. Furthermore, the excitation-intensity-dependent TA dynamics of the copolymers and BHJs is investigated, revealing that, when sufficiently high excitation intensity is used to induce annihilation processes, the fluorinated copolymers and BHJs incorporating the fluorinated copolymers show more rapid TA decay ascribable to morphological enhancement. These TA spectroscopic findings are found to correlate with the device characteristics with respect to fluorinated content in the polymer solar cells. In particular, both the short-circuit current density and fill factor of BHJ solar cells correspond closely with the fast decay parameters of the BHJ films under high excitation intensity.